MolAtom : atom inside a Molecule. More...
Collaboration diagram for ObjCryst::MolAtom:
Public Member Functions | |
| MolAtom (const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name, Molecule &parent) | |
| Constructor for a MolAtom. | |
| virtual | ~MolAtom () |
| Destructor. More... | |
| void | SetName (const string &name) |
| const string & | GetName () const |
| string & | GetName () |
| const Molecule & | GetMolecule () const |
| Molecule & | GetMolecule () |
| const REAL & | X () const |
| const REAL & | Y () const |
| const REAL & | Z () const |
| REAL & | X () |
| REAL & | Y () |
| REAL & | Z () |
| REAL | GetX () const |
| REAL | GetY () const |
| REAL | GetZ () const |
| REAL | GetOccupancy () const |
| void | SetX (const REAL) const |
| Set the X,Y,Z coordinate - this is const because sometimes their coordinate must be changed even though the atom does not move, if the atom is part of a rigid group (its position is then described by a combination of atomic cooordinates, plus a global translation and rotation... | |
| void | SetY (const REAL) const |
| void | SetZ (const REAL) const |
| void | SetOccupancy (const REAL) |
| bool | IsDummy () const |
| Returns true if this is a dummy atom, i.e. More... | |
| const ScatteringPower & | GetScatteringPower () const |
| void | SetScatteringPower (const ScatteringPower &) |
| virtual void | XMLOutput (ostream &os, int indent=0) const |
| virtual void | XMLInput (istream &is, const XMLCrystTag &tag) |
| void | SetIsInRing (const bool r) const |
| Flag this atom as being in a ring (or not). More... | |
| bool | IsInRing () const |
| void | SetNonFlipAtom (const bool nonflip) |
| Set a flag to prevent the atom's absolute configuration to be changed. More... | |
| bool | IsNonFlipAtom () const |
| Can this atom be flipped (return=false) or should its absolute configuration be kept (return=true) | |
| size_t | int_ptr () const |
| Access to the integer address of this object, for unique identification from python. | |
Private Attributes | |
| string | mName |
| Name for this atom. | |
| REAL | mX |
| Cartesian oordinates in the Molecule reference frame. More... | |
| REAL | mY |
| REAL | mZ |
| REAL | mOccupancy |
| Occupancy. | |
| const ScatteringPower * | mpScattPow |
| ScatteringPower. | |
| Molecule * | mpMol |
| Parent Molecule. | |
| bool | mIsInRing |
| Is the atom in a ring ? | |
| bool | mIsNonFlipAtom |
| Can the atom be flipped (this is used for optically active atom which should keep their absolute configuration. | |
Detailed Description
MolAtom : atom inside a Molecule.
This keeps coordinates, recorded in a cartesian frame (in Angstroem), the associated scattering power and it also keeps in a list of all bonds in which this atom is involved.
- Note
- maybe it's not a great idea to keep a reference of bonds for this atom in here
Definition at line 58 of file Molecule.h.
Constructor & Destructor Documentation
◆ ~MolAtom()
|
virtual |
Destructor.
Tells the parent Molecule and all Bond that it is being destroyed.
Definition at line 201 of file Molecule.cpp.
Member Function Documentation
◆ IsDummy()
| bool ObjCryst::MolAtom::IsDummy | ( | ) | const |
Returns true if this is a dummy atom, i.e.
without an associated scattering power.
Dummy atoms can be used to mark positions, or for restraints.
Definition at line 252 of file Molecule.cpp.
◆ SetIsInRing()
| void ObjCryst::MolAtom::SetIsInRing | ( | const bool | r | ) | const |
Flag this atom as being in a ring (or not).
This is a const method because the existence of a ring is only a consequence of the connectivity of the Molecule.
Definition at line 344 of file Molecule.cpp.
◆ SetNonFlipAtom()
| void ObjCryst::MolAtom::SetNonFlipAtom | ( | const bool | nonflip | ) |
Set a flag to prevent the atom's absolute configuration to be changed.
- Parameters
-
nonflip if true, the atom.
This should only be changed by Molecule::AddNonFlipAtom() and Molecule::RemoveNonFlipAtom()
Definition at line 347 of file Molecule.cpp.
Member Data Documentation
◆ mX
|
mutableprivate |
Cartesian oordinates in the Molecule reference frame.
mutable because they may need to be changed when in a rigid group, even though the end position of the atom remains the same.
Definition at line 133 of file Molecule.h.
The documentation for this class was generated from the following files:
